A New Beginning
by AntoniaRose
Summary: Thomas and Teresa's life after The Death Cure, if Teresa had survived
1. Chapter 1

_Hey everyone. This is my first fanfic for The Maze Runner._

_Warning: Please only read this fanfic if you have finished all three books, as it contains a lot of spoilers. DO NOT read beyond this point if you have not finished the trilogy yet. If you choose to disregard this warning, it is entirely your choice. End of warning. _

_Now, to business. I would like to clarify that in this fanfic, Newt, Minho, Teresa, Thomas, Gally, and Frypan are all alive and well. As this is a fanfic about Thomas and Teresa, Brenda was the one who died saving Thomas. This is after the events of The Death Cure. _

_Although Thomas thought he shot Newt, it shall be revealed that that was not the case. _

**Please enjoy. **

Chapter One: Discovery

Thomas had thought he was done with WICKED's mind games. He had thought that it was all over-the Trials, the deaths, the doubt.

He should never have trusted WICKED.

Then he wouldn't have been staring into the eyes of a ghost.

Thomas had seen countless of his friends die. He had held Chuck in his arms as life ebbed away from the boy. He had seen Brenda push him out of the way of a falling chunk of rock, sacrificing her life to save his. He had been asked to shoot one of his best friends in the head.

Or so he thought.

WICKED had revealed that Newt, one of the few boys that Thomas had first seen in the Maze, was not immune to the Flare. The Flare-the terrible disease that thrived in the human brain, that destroyed a person's humanity, turning them into less than animals.

Newt had started the journey along that path, and Thomas and Minho had watched helplessly as their friend had slipped away from them.

Newt had asked Thomas, in a final, desperate, gesture, to kill him. Shoot him in the head and put him out of his misery.

Let him leave the world before he lost his sanity, went past the Gone. Went to a place from which he could never come back.

And Thomas had done it. With one last burst of energy, he had pulled the trigger.

Newt was dead.

But if that was the case, he shouldn't have been staring at the boy's face.

His mind reeled to the events of the morning….

"Here again?"

Thomas turned to see the speaker, already knowing who it was. Teresa-her blue eyes seeming to glow in the dark. She walked forward to sit beside him, her legs hanging off the edge of the cliff, facing the ocean. She didn't say anything, but she took his hand and squeezed it.

Thomas forced himself to speak. "I was remembering the time before the Flare-it was devastation, but the world would have pulled through. If the Flare just hadn't spread, maybe I would still have my parents."

Teresa was silent for a long time. "You know I got the Swipe removed," she said quietly in a low voice. Thomas looked at her, urging her to continue.

She looked away from him. "I saw what happened. I remember these four people-Mark, Trina, Lana and Alec. The Flare didn't spread by itself Tom. Mark, Trina…they all lived before the sun flares. Alec got them out, along with a couple of others, when the flares hit.

They travelled overland, all the way to the Andes. That's where they stayed. And then, one day, WICKED decided that there were too many people, and too little resources.

They had developed the Flare as a means of population control. They expected it to shut down the brain quickly, provide a fast death."

Thomas was shaking with anger. Teresa didn't seem to notice, but he saw the hardness in her jaw, and he knew that she was just as angry as him.

"But then something happened that they hadn't planned for," Teresa continued. "The virus mutated as it spread from person to person. The first few died quickly, but as it spread, faster and faster, the symptoms took longer to show, and by the time people started quarantining the infected around them, they had already caught the virus."

"This group of four-they ran away after their settlement was destroyed by WICKED. The same thing happened to my family. But, by the time they left, my parents had caught the Flare, and they started losing their humanity."

Teresa's voice trembled. "They thought I was a devil, because I wasn't sick, although I got hit by one of the Flare darts. They abandoned me. Trina and the others took care of me, when I was running from Cranks."

Thomas looked at Teresa, and noticed tears in her blue eyes.

"But they weren't immune, Tom. They caught the Flare, just like everyone else. They held it off as long as they could. WICKED left the East when they saw what happened. Trina and Mark…they knew that they had to save me."

"They got me to a Flat Trans, just as the last WICKED member went through. Mark…he told me to be brave. He scribbled a note, telling them I was immune. He told me to go through the Flat Trans to be brave."

Teresa was sobbing. "There were a couple of Cranks who wanted to fight WICKED. Mark told me to run. I stopped just at the last possible minute, just before Alec crashed the Berg into the building. I remember their last moments-they never left each other. They were hugging, as tightly as possible. That was the last time I ever saw them."

"They sacrificed themselves so I could live. I'll never forget them."

Thomas gently drew Teresa close to him, and stroked her hair as she quietly sobbed. Eventually, she quietened, and they sat together in companionable silence. "I'm really sorry about Brenda," Teresa said softly. "I know she was the only person you could trust when I…when I betrayed you."

He nodded, surprised to feel tears rolling down his cheeks. "It doesn't matter," he told her. "Brenda chose to save me, just like Chuck did. I'll never forget them, but I can't waste my life mourning them either. I have to accept and move on. The dead can't come back."

Ironically, that was when Minho had come running up the cliff yelling at the top of his lungs. He stopped when he saw Thomas and Teresa hugging, but he didn't even tease Thomas about it. He just ran towards them and yanked him up.

"What's wrong, Minho?" Thomas asked. The boy's eyes were wide with fear, and horror. "You have to see," his friend replied, his voice full of fear. He turned and ran down the cliff, with Thomas and Teresa hot on his heels.

He stopped right beside the mess hall, at the place where they had come through the Flat Trans, leaving the Flare-infected world behind them once and for all. A group of boys were huddled around something-a person. Frypan was leaning down over the person. He looked up, and beckoned Thomas forward.

Thomas knelt down beside Frypan, and his legs buckled when he realised who was the person who was lying on the ground, exhausted. A face he had thought was lost to him forever.

The boy smiled weakly. "Tommy," he whispered.

And then Thomas knew, without a doubt, who it was. His heart filled with fear, horror, and a small part of joy.

It was Newt.

Thomas was staring at Newt's face blankly. Minho had taken charge, telling them to move Newt to a bunker. Minho and Thomas had carried Newt to their own empty bunker, and got him some food.

Newt had sat up, and was just finishing sipping his water. Thomas had been staring at his face since he had first seen the boy. He was pretty sure Minho was doing the same.

His mind kept replaying the last time he had seen Newt-the boy had begged him to kill him, pleading with him. And, finally, Thomas had granted that wish, although it had broken his heart.

But Newt was sitting here, perfectly fine.

It had taken all of Thomas's courage to tell Minho what he had done to Newt. And, surprisingly, the boy had understood. He had patted Thomas on the back and left him to his thoughts.

Which Thomas had appreciated. If Minho had made any smart comment then, Thomas didn't think he would have been alive.

But if all that was true….how on Earth was Newt sitting in front of them-eating and drinking and breathing?

Thomas had no clue what to make of it. He was half convinced that he was in a dream. Or WICKED was just testing them. Again.

Newt seemed to understand what was going on in their minds. He smiled at Thomas and passed him a piece of paper. Thomas's heart contracted. He remembered the last few times Newt had left them notes…he wasn't exactly eager to get another.

If Newt was going to ask Thomas to kill him after Thomas had just got him back, Thomas was seriously going to lose it, Flare or no Flare.

Newt laughed. "I shucking swear Tommy. It's not a bloody suicide note."

Relieved, Thomas took the piece of paper from him.

He opened it. His eyes at once flashed to the sender, and a shiver ran up his spine. The letter writer's name was familiar, even though Thomas had never met her. Thomas read the letter aloud:

_WICKED Headquarters_

_4__th__ October 2320 _

_Dear Thomas, _

_I know you are shocked and confused right now. I know what you must be thinking. But I assure you, Thomas, this is not a Trial. WICKED is finished. I don't know if you realize, but it has been three years since you left this world-once and for all. Three long, hard and difficult years, that you have been spared. _

_With all our efforts, we have not succeeded. The world has succumbed to the Flare. The Flare has mutated, and spread faster and faster, bringing with it insanity-and death. The Flare, at least, brings with it now the merciful bliss of death, allowing us one grasp of hope. The human race has been wiped out. _

_I am horrified to say this-but, at this moment, I am the only person alive who has a minimal grasp of sanity, apart from Mr Newton. But not for long-even as I write, I feel the madness beginning in my brain, and I see insanity and death speeding towards me. I only wish that I will soon leave this world, and my suffering will not last long. _

_Soon, the world will be empty, without the presence of human beings, except for the two hundred or so people with you, Thomas. All I can ask of you now, is that you begin civilisation anew. You are all immune-start a new human race, and learn from the mistakes we have made. _

_I am sorry that we put you through such hardship-in the Maze, the Scorch, and even after. I am sorry that you suffered so much more than any child has a right to suffer, and I am sorry that you witnessed things that no child should ever have to witness. All I ask is for your forgiveness, and the promise to begin the human race again. I wish you the best. _

_I don't know how history will view us, but now, in my defence, all I can say, is that WICKED had only one purpose, and that was to save the human race, at any cost. _

_And for that sole reason, WICKED is good. _

_Chancellor Ava Paige_

Thomas finished reading, horror sweeping through him. He had never imagined that the whole world would be wiped out. He looked up to see the same shock on Minho's, but Newt's expression showed only sadness.

Evidently, he had witnesses the long, arduous process first hand. Thomas looked up at him, and asked silently the question he could not put into words. Newt nodded, and leant forward.

Thomas finally broke the silence that stretched between the three of them. "Newt, how-I mean, did you know what-"

Newt interrupted him. "Yeah, I saw. I was the one controlling myself, if you know what I mean."

Thomas and Minho looked at each other in confusion. "I wasn't there, you know?" Newt explained. "After the Scorch, they took me away. They said that Thomas and Teresa were the Final Candidates-whatever that meant-and they said they needed to put in place a final variable to see how Thomas reacted."

"They wanted to know how Thomas would respond if he had to kill one of his closest friends. I am actually immune, but they put a holographic image in place of me-remember when we thought those rescuers were killed, and then all their bodies vanished?"

Thomas remembered that all too well. He shuddered as he remembered the grotesque swelling and smell of the bodies.

"Yeah, they can manipulate the smell and sight of the image as well. None of those shanks were actually killed, you know? It was just a shucking hologram."

"So they put me in charge of the "fake Newt", and made me control him," Newt explained.

Thomas felt himself turn red when he remembered what he had done to Newt-and it hadn't even been the real Newt!

"So you saw what I did?" Thomas questioned. Newt nodded, and patted Thomas on the shoulder. "Don't worry, Tommy, I don't judge you. That must have taken a great deal of courage."

"Thanks," Thomas muttered.

"Anyway, I kept the hologram-with the fake blood flowing-in place until you guys drove off. Then I just dissipated it. The other Cranks were too far gone to notice anything abnormal."

Thomas felt his heart explode with relief. Newt really was back-it wasn't a Trial, and they were all free.

They were free.


	2. Chapter 2

_Hey guys! I am so glad to be writing the second chapter, and I have to say-I am amazed that I got a review so soon. I expected that no one would ever read my fanfic, out of the thousands out there, and I am honoured and grateful, that people actually choose to read mine. I want to say thank you to Nic923, for your kind words. You have no idea how you made my day and motivated me to start the second chapter. Thomas and Teresa fans, you will love this. _

_And so…enjoy. _

Chapter Two: Relationship

"THOMAS!"

Thomas turned as he heard Teresa calling his name. He waited for her to catch up, as she reached his side, quickly grabbing his arm and staring at him with excited blue eyes.

"I just heard. Tom-is it true?" she asked him.

He nodded, and Teresa's eyes filled with tears. She surprised him by giving him a sudden hug, and he patted her on the back, before she sank to the ground.

He had not yet told Teresa what had happened to Newt. He knew that she had just thought that Newt had become a Flare-infected Crank, and eventually died. He didn't have the guts to tell her, and now that it didn't matter-that Newt was alive-why should he?

Unfortunately, at that moment he looked down to see that Teresa was staring at him. And somehow, her expression told him that she suspected what he had done.

She searched his eyes, and he nodded slightly, staring at the ground. He felt her finger under his chin, and she lifted his face up, and stared into his eyes-blue into brown.

Thomas looked into her eyes, and he was surprised at what he found there. He found compassion, sympathy, and most of all….understanding. That was when he realized that Teresa was truly the person who understood him, better than anyone.

Perhaps it was just because he knew her before the Glade, or he was just too shaken from his experience, but a strange feeling swept through him. All he knew, was that he just wanted to kiss her.

He pulled her around the corner and towards him. She stared at him for a moment, and then she was pressed against him, her fingers tangled in his hair, brushing his cheek, their lips connected.

He moved his hands to her waist and held her close to him as he kissed her, knowing at that moment what he wanted, what he had denied himself the past three years due to his guilt about Brenda.

He had to tell Teresa his feelings, show her that he fully trusted her once more, understanding-finally-that what she had done had been for him, and just for him.

Thomas realized that over the past three years, Teresa had once again become his best friend, the way she had been in the Glade, and even before. But he no longer wanted her as a friend. He wanted her as something more.

Thomas could feel the heat between the two of them. He didn't know how much longer they could last without breaking for air, but he found that he didn't want to pull away from her.

He pressed her closer to him, and he moved one of his hands up to cup her head, her hair ruffling his face as a breeze blew past them.

All that seemed to exist was Teresa, her hair, her sweet, fresh smell, the feeling of her hair on his face, her soft, warm lips on his….

"AHEM!"

Flushed, Thomas immediately pulled away, Teresa doing the same thing. They both turned to the source of the sound, and saw Minho and Newt standing there, exchanging glances and smirking.

"What?" Thomas snapped, feeling his cheeks turn red as Teresa awkwardly stood beside him.

"Well…" Minho stretched the word out, slowly walking towards them. "Newt just told me something, and we were looking all the bloody place for you. We were just about to send out a search party when we found you two…apparently very busy.

Sorry to interrupt your very hot making out session, but we were standing there for five minutes waiting to see if you shanks were going to break apart. Apparently not."

Minho shrugged, and Thomas felt his cheeks burning with embarrassment. "Well, Minho what is this super important thing that you have to tell me?" he asked, moving towards his friend, arms folded.

"Right…that. Apparently, we don't have to worry about any Cranks coming through the way Newt did. The world collapsed. No one knows how to operate a Flat Trans anymore. Anyway, this….Ava Paige…she sealed the Trans and destroyed it once Newt was through."

Thomas waited.

Then he realized that Minho had finished speaking.

"WHAT?" he yelled. "You SLINTHEAD! You did it on purpose!"

Minho was laughing too hard to reply, and even Newt was doubled over in laughter. Thomas shook his head at the both of them, too embarrassed to turn around and face Teresa.

"Well, now, how could we miss this golden opportunity? You shank, did you seriously think we didn't see you going off with your shuck girlfriend?" Minho asked, his eyes dancing with mirth.

Teresa walked off, shaking her head. "Immature idiots," she muttered as she strode off. "Thomas, you shank-go after her," Newt hissed. "I think she's angry."

Thomas didn't need to be told twice. He dashed after her, only to find her walking towards the mess hall. Of course-it was nearly dinnertime! He steeled himself.

He would just have to say it.

He reached her just before she walked into the hall. "Teresa! Wait, I need to talk to you."

She didn't look at him. "There's nothing to talk about, _Thomas_." The way she said his name stung a bit-as if she was disgusted with him.

She walked inside the hall.

He blocked her way. "Teresa-you have to listen to me." She glanced at him, and her eyes were wet with tears.

"Thomas, please don't make this harder than it already is. It was just a mistake, that's all. I know you love Brenda. I was wrong. Please-let's just forget about it."

Thomas stared at her blankly. She thought he loved _Brenda_? She thought that he didn't have feelings for her-that he had never had feelings for her?

He grasped her hands and looked into her eyes-her beautiful blue eyes. "Teresa," he said sincerely. "Please believe me. I love _you_, not Brenda. I never really loved Brenda. She was nothing more than a friend to me. _You _are the one I love."

Teresa shook her head. "Tom, I betrayed you. You can never trust me, never love me. Please stop lying."

Thomas was in despair. How was he supposed to make Teresa believe that he was telling the truth?

Suddenly an idea struck him. He turned to the mess hall, which was bustling with activity. He prepared himself.

"EVERYONE!" he yelled as loudly as he could. All eyes in the room turned to him, as, out of the corner of his eye, he saw Minho and Newt sidle into the room.

"I'm sorry, but I need your help," he said. "You see, this beautiful girl here," he indicated Teresa, "will just not believe me when I say that I love her. This is the only way I can think of to show her I'm telling the truth."

He turned to Teresa. "Teresa?" he asked, his voice trembling slightly. "I love you, I really do. Will you be my girlfriend?"

The moment seemed suspended in time. The whole hall seemed to be collectively holding their breath as he waited for Teresa's reply.

"Yes," she replied softly, her eyes welling with more tears. Then she hurled herself at him, and wrapped her legs around his torso, pressing her lips to his once more.

At that the whole room burst into applause, whoops and cheers. The noise was deafening, but Thomas made out Minho and Newt yelling "Go Thomas!"

But at that moment, he didn't care.

All he cared about was the girl he loved, who was kissing him, finally in his arms.

Teresa.

_So, how was it my dear readers?(or reader, depends) I hope you enjoyed it, Thomesa fans! Love you guys, and till next time, take care!_


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